Three weeks into Jack's prison stay, Jiminez visited Teri Bauer at her home, hoping to learn why Jack supposedly killed Adrian Tintfass. Teri was unable to help, but reminded him that her husband was capable of anything. As he left, Jiminez was stopped by two FBI agents, Jason Fujimora and Holmquist, who warned him to back off the Bauer case but refused to elaborate.

Later that night, Jack Bauer was forced to break out of the prison with Emil Ramirez, his link to Zapata. After Henderson refused to provide him assistance, Jack was forced to call Teri and ask her to bring him an emergency bag from their garage to a restaurant where they had once had a fight. Jiminez tracked Teri to the restaurant and informed Smiley Lopez, who sent a hit squad to perform a drive-by shooting against the Bauers and Ramirez. However, the attack was driven away when Jack returned fire.

After Jack conducted an arms exchange with Jemaah Islamiyah at the U-Pack Storage Facility, Jiminez arrived to coordinate the clean-up. Tony Almeida, who had been undercover with the Indonesians, shared his suspicion that Jack had turned traitor and was selling his government access for profit, but Jiminez claimed that it was impossible.

After U.S. marshal Dan Pascal took Jack into custody at the Biltmore Hotel, Jiminez rammed his car so that he could free Jack. In actuality, he was planning to kill Jack and dump his body somewhere, but Bauer overpowered Jiminez and stole his car.

Later in the morning, Jack had to go undercover with Sergei Petrenko's crew, posing as drug dealer Felix Studhalter. After Tony and Nina Myers apprehended Studhalter in Los Feliz, Jiminez arrived at the house and announced that he had been assigned to transport him back to CTU, while Nina and Tony were to oversee security at the Pacific Rim Forum. Jiminez intentionally let Studhalter go free, knowing that he would call Petrenko and blow Jack's cover. He claimed to Ryan Chappelle that Studhalter had overpowered him and escaped. Next, he went to Smiley Lopez's house in Boyle Heights and killed the MS-13 leader, so that he couldn't point to Henderson as the man who hired him to kill Jack inside the prison.

After Becker called Henderson to schedule their interview, Henderson angrily called Jiminez up to his office and demanded to know why he had repeatedly failed to kill Jack. Saying that time was almost up, Henderson ordered Jiminez to follow Jack to the Staples Center, where Zapata was planning to assassinate Martin Webb.

At the convention center, Jiminez had Jamey Farrell call Jack and tell him that Jiminez urgently needed to meet with him in the basement regarding the Zapata operation. When Jack arrived, Jiminez shot him in the shoulder, but Jack, stunned at the betrayal, managed to throw him off balance. After a brutal fight, Jack managed to grab Peter's gun and shot him three times in the back.

While Jiminez was at the Staples Center, Henderson altered CTU's phone records to alter his calls to Smiley Lopez so that they appeared to have come from Jiminez's phone. This effectively framed Jiminez as the sole party behind Jack's attempted murder. (Chaos Theory)